[Bioc-devel] problems installing cran dependencies with BioC devel in mac

Dan Tenenbaum dtenenba at fredhutch.org
Wed Nov 30 23:06:17 CET 2016



----- Original Message -----
> From: "Sean Davis" <seandavi at gmail.com>
> To: "Martin Morgan" <martin.morgan at roswellpark.org>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Wednesday, November 30, 2016 1:20:58 PM
> Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC devel in mac

>> On Nov 30, 2016, at 4:13 PM, Martin Morgan <martin.morgan at roswellpark.org>
>> wrote:
>> 
>> On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote:
>>> Full transcript please; you're compiling from source.
>> 
>> Excuse my ignorance about the Mac world but shouldn't these be available for
>> binary installation via the URL Andrea provided,
>> 
>>  https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/
>>  <https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/>
> 
> I am not sure if it is supposed to be, but this directory is empty.
> 

Building binaries of packages for R-devel is not always CRAN's highest priority, but it could be worth asking about. Simon Urbanek is the Mac person at CRAN.

Dan


> Sean
> 
> 
>> 
>> ?
>> 
>> Martin
>> 
>>> 
>>> On Wed, Nov 30, 2016 at 8:24 AM, Rodriguez Martinez, Andrea <
>>> andrea.rodriguez-martinez13 at imperial.ac.uk> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> 
>>>> Thanks for your reply.  Maybe I am doing something wrong, but I do get
>>>> errors, after I select the option install from source. See below:
>>>> 
>>>> 
>>>>> source("https://bioconductor.org/biocLite.R")
>>>>> biocLite("MWASTools")
>>>> 
>>>> 
>>>> The downloaded source packages are in
>>>> ‘/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs80000gn
>>>> /T/Rtmp79qF9E/downloaded_packages’
>>>> Warning messages:
>>>> 1: In install.packages(pkgs = doing, lib = lib, ...) :
>>>>  installation of package ‘SparseM’ had non-zero exit status
>>>> 2: In install.packages(pkgs = doing, lib = lib, ...) :
>>>>  installation of package ‘irlba’ had non-zero exit status
>>>> 3: In install.packages(pkgs = doing, lib = lib, ...) :
>>>>  installation of package ‘minqa’ had non-zero exit status
>>>> 4: In install.packages(pkgs = doing, lib = lib, ...) :
>>>>  installation of package ‘RcppEigen’ had non-zero exit status
>>>> 5: In install.packages(pkgs = doing, lib = lib, ...) :
>>>>  installation of package ‘quantreg’ had non-zero exit status
>>>> 6: In install.packages(pkgs = doing, lib = lib, ...) :
>>>>  installation of package ‘lme4’ had non-zero exit status
>>>> 7: In install.packages(pkgs = doing, lib = lib, ...) :
>>>>  installation of package ‘pbkrtest’ had non-zero exit status
>>>> 8: In install.packages(pkgs = doing, lib = lib, ...) :
>>>>  installation of package ‘car’ had non-zero exit status
>>>> 9: In install.packages(pkgs = doing, lib = lib, ...) :
>>>>  installation of package ‘igraph’ had non-zero exit status
>>>> 10: In install.packages(update[instlib == l, "Package"], l, repos =
>>>> repos,  :
>>>>  installation of package ‘mgcv’ had non-zero exit status
>>>> 
>>>> 
>>>>> sessionInfo()
>>>> R Under development (unstable) (2016-10-26 r71594)
>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>> Running under: OS X El Capitan 10.11.6
>>>> 
>>>> locale:
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>> 
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>> 
>>>> other attached packages:
>>>> [1] BiocInstaller_1.25.2
>>>> 
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_3.4.0
>>>> 
>>>> 
>>>> 
>>>> Thanks very much in advance,
>>>> 
>>>> 
>>>> Best wishes,
>>>> 
>>>> 
>>>> Andrea
>>>> 
>>>> ________________________________
>>>> From: Vincent Carey <stvjc at channing.harvard.edu>
>>>> Sent: 30 November 2016 12:39:12
>>>> To: Rodriguez Martinez, Andrea
>>>> Cc: bioc-devel at r-project.org
>>>> Subject: Re: [Bioc-devel] problems installing cran dependencies with BioC
>>>> devel in mac
>>>> 
>>>> In fact there was a problem installing igraph from source, but that is
>>>> another issue.  That can
>>>> be resolved using the precompiled binary at http://igraph.org/r/#downloads
>>>> 
>>>> 
>>>>> sessionInfo()
>>>> 
>>>> R Under development (unstable) (2016-10-26 r71594)
>>>> 
>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>> 
>>>> Running under: OS X El Capitan 10.11.6
>>>> 
>>>> 
>>>> locale:
>>>> 
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>> 
>>>> 
>>>> attached base packages:
>>>> 
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>> 
>>>> 
>>>> other attached packages:
>>>> 
>>>> [1] BiocInstaller_1.25.2 MWASTools_0.99.10    rmarkdown_1.1
>>>> 
>>>> 
>>>> loaded via a namespace (and not attached):
>>>> 
>>>> [1] Rcpp_0.12.8                XVector_0.15.0
>>>> 
>>>> [3] GenomeInfoDb_1.11.6        nloptr_1.0.4
>>>> 
>>>> [5] ppcor_1.1                  plyr_1.8.4
>>>> 
>>>> [7] zlibbioc_1.21.0            tools_3.4.0
>>>> 
>>>> [9] boot_1.3-18                digest_0.6.10
>>>> 
>>>> [11] lme4_1.1-12                evaluate_0.10
>>>> 
>>>> [13] tibble_1.2                 gtable_0.2.0
>>>> 
>>>> [15] nlme_3.1-128               lattice_0.20-34
>>>> 
>>>> [17] mgcv_1.8-16                Matrix_1.2-7.1
>>>> 
>>>> [19] igraph_1.0.1               parallel_3.4.0
>>>> 
>>>> [21] SparseM_1.74               gridExtra_2.2.1
>>>> 
>>>> [23] stringr_1.1.0              IRanges_2.9.8
>>>> 
>>>> [25] S4Vectors_0.13.2           MatrixModels_0.4-1
>>>> 
>>>> [27] stats4_3.4.0               grid_3.4.0
>>>> 
>>>> [29] nnet_7.3-12                Biobase_2.35.0
>>>> 
>>>> [31] qvalue_2.7.0               minqa_1.2.4
>>>> 
>>>> [33] ggplot2_2.2.0              reshape2_1.4.2
>>>> 
>>>> [35] car_2.1-3                  glm2_1.1.2
>>>> 
>>>> [37] magrittr_1.5               GenomicRanges_1.27.12
>>>> 
>>>> [39] scales_0.4.1               htmltools_0.3.5
>>>> 
>>>> [41] MASS_7.3-45                splines_3.4.0
>>>> 
>>>> [43] BiocGenerics_0.21.0        assertthat_0.1
>>>> 
>>>> [45] pbkrtest_0.4-6             SummarizedExperiment_1.5.3
>>>> 
>>>> [47] colorspace_1.3-1           quantreg_5.29
>>>> 
>>>> [49] stringi_1.1.2              lazyeval_0.2.0
>>>> 
>>>> [51] munsell_0.4.3
>>>> 
>>>> On Wed, Nov 30, 2016 at 7:27 AM, Vincent Carey <stvjc at channing.harvard.edu
>>>> <mailto:stvjc at channing.harvard.edu>> wrote:
>>>> sessionInfo()?  I just did biocLite("MWASTools") with a devel version of
>>>> R/BiocInstaller,
>>>> and it seems to work well.
>>>> 
>>>> On Wed, Nov 30, 2016 at 6:04 AM, Rodriguez Martinez, Andrea <
>>>> andrea.rodriguez-martinez13 at imperial.ac.uk<mailto:andrea.
>>>> rodriguez-martinez13 at imperial.ac.uk>> wrote:
>>>> Hi,
>>>> 
>>>> 
>>>> I'm trying to install my MWASTools package (devel branch) in mac, and I
>>>> get a lot of errors regarding the installation of the dependencies from
>>>> CRAN because there are no files in the repository:
>>>> 
>>>> https://cran.rstudio.com/bin/macosx/mavericks/contrib/3.4/
>>>> 
>>>> 
>>>> For windows, I dont have any problems with the installation because the
>>>> cran repository has the files:
>>>> 
>>>> https://cran.rstudio.com/bin/windows/contrib/r-devel/
>>>> 
>>>> 
>>>> One solution, is to install the CRAN dependencies in advance using
>>>> 
>>>>> install.packages(pkgs, contriburl = "https://cran.rstudio.com/bin/
>>>> macosx/mavericks/contrib/3.3/")
>>>> 
>>>> 
>>>> I wonder if there is another solution to do this directly from biocLite.
>>>> 
>>>> 
>>>> Thanks very much,
>>>> 
>>>> 
>>>> Andrea
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
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